R Notebook

Last updated: 2019-02-19

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  Ignored files:
      Ignored:    analysis/figure/
      Ignored:    code/.ipynb_checkpoints/
      Ignored:    data/
      Ignored:    output/10x-180504
      Ignored:    output/10x-180504-aligned
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      Modified:   plots/supplementary_figures/sfig_180504_pcelbow.pdf
      Modified:   plots/supplementary_figures/sfig_180504_qcplots.pdf
  
  

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#library(workflowr, lib.loc='/home/cbmr/pytrik/libraries/')
#library(Seurat, lib.loc='/home/cbmr/pytrik/libraries/')

seurobj <- readRDS('output/10x-180831')

PC2 seems to capture the difference between Monocle states.

DimPlot(seurobj, group.by='State', reduction.use='pca', dim.1=5, dim.2=2)

How are some of the branch-dependent genes expressed? Brown genes

FeaturePlot(seurobj, features.plot=c('UCP2', 'FABP5', 'GPD1', 'ADIPOQ'), reduction.use='pca', dim.1=5, dim.2=2, cols.use=c('gray', 'blue'), no.legend=F, nCol=2)

White genes

FeaturePlot(seurobj, features.plot=c('APOD', 'MGP', 'IGF2', 'PLAC9'), reduction.use='pca', dim.1=5, dim.2=2, cols.use=c('gray', 'blue'), no.legend=F, nCol=2)

Expression of brown branch genes in the t-SNE

FeaturePlot(seurobj, features.plot=c('UCP2', 'FABP5', 'SCD', 'G0S2', 'ADIPOQ', 'GPD1', 'PLIN1', 'PLIN4'), reduction.use='tsne', cols.use=c('gray', 'blue'), no.legend=F, nCol=2)

Some of the white branch genes

FeaturePlot(seurobj, features.plot=c('APOD', 'MGP', 'DCN', 'PLAC9', 'IGF2', 'ZFP36', 'FOS',
'TCEAL4',
'C1R',
'OSR2',
'MFGE8',
'FBLN1',
'CLU'), reduction.use='tsne', cols.use=c('gray', 'blue'), no.legend=F, nCol=2)

PC2 heatmap

PCHeatmap(seurobj, pc.use=2, cells.use=100, do.balanced = T, num.genes = 100)

Warning in heatmap.2(data.use, Rowv = NA, Colv = NA, trace = "none", col = col.use, :
Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.

Warning in heatmap.2(data.use, Rowv = NA, Colv = NA, trace = "none", col = col.use, :
Discrepancy: Colv is FALSE, while dendrogram is `column'. Omitting column dendogram.

Warning in plot.window(...): "dimTitle" is not a graphical parameter

Warning in plot.xy(xy, type, ...): "dimTitle" is not a graphical parameter

Warning in title(...): "dimTitle" is not a graphical parameter

FeaturePlot(seurobj, features.plot=c('ADIPOQ', 'LIPE', 'PLIN4', 'FASN', 'AGPAT2', 'PCK1', 'MMP2', 'PPAP2B', 'SCARA5', 'IGFBP6', 'SERPING1'), reduction.use='tsne', cols.use=c('gray', 'blue'), no.legend=F, nCol=2)

FeaturePlot(seurobj, features.plot='EBF2', cols.use=c('gray', 'blue'), no.legend=F)

Session information

sessionInfo()

R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Storage

Matrix products: default
BLAS: /nfsdata/tools/R/3.4.3/lib64/R/lib/libRblas.so
LAPACK: /nfsdata/tools/R/3.4.3/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Seurat_2.3.4    Matrix_1.2-15   cowplot_0.9.4   ggplot2_3.1.0   workflowr_1.1.1

loaded via a namespace (and not attached):
  [1] Rtsne_0.13          colorspace_1.4-0    class_7.3-14        modeltools_0.2-22  
  [5] ggridges_0.5.0      mclust_5.4.1        rprojroot_1.3-2     htmlTable_1.12     
  [9] base64enc_0.1-3     rstudioapi_0.9.0    proxy_0.4-22        flexmix_2.3-14     
 [13] bit64_0.9-7         mvtnorm_1.0-8       codetools_0.2-16    splines_3.4.3      
 [17] R.methodsS3_1.7.1   robustbase_0.93-2   knitr_1.20          jsonlite_1.6       
 [21] Formula_1.2-3       ica_1.0-2           cluster_2.0.7-1     kernlab_0.9-27     
 [25] png_0.1-7           R.oo_1.22.0         compiler_3.4.3      httr_1.3.1         
 [29] backports_1.1.2     assertthat_0.2.0    lazyeval_0.2.1      lars_1.2           
 [33] acepack_1.4.1       htmltools_0.3.6     tools_3.4.3         bindrcpp_0.2.2     
 [37] igraph_1.2.2        gtable_0.2.0        glue_1.3.0          RANN_2.6           
 [41] reshape2_1.4.3      dplyr_0.7.6         Rcpp_0.12.18        trimcluster_0.1-2.1
 [45] gdata_2.18.0        ape_5.1             nlme_3.1-137        iterators_1.0.10   
 [49] fpc_2.1-11.1        gbRd_0.4-11         lmtest_0.9-36       stringr_1.3.1      
 [53] irlba_2.3.2         gtools_3.8.1        DEoptimR_1.0-8      MASS_7.3-50        
 [57] zoo_1.8-3           scales_1.0.0        doSNOW_1.0.16       parallel_3.4.3     
 [61] RColorBrewer_1.1-2  yaml_2.2.0          reticulate_1.10     pbapply_1.3-4      
 [65] gridExtra_2.3       rpart_4.1-13        segmented_0.5-3.0   latticeExtra_0.6-28
 [69] stringi_1.2.4       foreach_1.4.4       checkmate_1.8.5     caTools_1.17.1.1   
 [73] bibtex_0.4.2        Rdpack_0.9-0        SDMTools_1.1-221    rlang_0.3.1        
 [77] pkgconfig_2.0.2     dtw_1.20-1          prabclus_2.2-6      bitops_1.0-6       
 [81] evaluate_0.11       lattice_0.20-38     ROCR_1.0-7          purrr_0.2.5        
 [85] bindr_0.1.1         labeling_0.3        htmlwidgets_1.2     bit_1.1-14         
 [89] tidyselect_0.2.4    plyr_1.8.4          magrittr_1.5        R6_2.4.0           
 [93] snow_0.4-2          gplots_3.0.1        Hmisc_4.1-1         whisker_0.3-2      
 [97] pillar_1.3.1        foreign_0.8-71      withr_2.1.2         fitdistrplus_1.0-9 
[101] mixtools_1.1.0      survival_2.42-6     nnet_7.3-12         tsne_0.1-3         
[105] tibble_2.0.1        crayon_1.3.4        hdf5r_1.0.0         KernSmooth_2.23-15 
[109] rmarkdown_1.10      grid_3.4.3          data.table_1.11.4   git2r_0.24.0       
[113] metap_1.0           digest_0.6.16       diptest_0.75-7      tidyr_0.8.1        
[117] R.utils_2.7.0       stats4_3.4.3        munsell_0.5.0      

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